This new release 0.3.2 has been extensively validated to check that the results match those of the original implementation, and includes some important optimizations. The first is the use of NumPy for internal data representation and calculations, and the second is the possibility to use multi-core processors to run the most expensive part in parallel. Moreover, the command line interface has been improved, and now is quite flexible and easy to use.

This new OncodriveFM depends on numerical Python libraries (numpy, scipy, statsmodels) that have to be installed previously in order to work. There is a detailed documentation in the Bitbucket repository that specifies how to install the dependencies, how to download and install OncodriveFM, and how to run the included example.

IntOGen SM 2.0.0 uses OncodriveFM version 0.2. There have been some bug fixes and performance improvements since that version of OncodriveFM. We are about to release a new version of OncodriveFM that includes the possibility to use the mean as test estimator. We are also about to release a new version of IntOGen SM (2.1.0) that uses the latest OncodriveFM version using the mean estimator, fixes some installation problems, and implements new features (most probably during this week or the next one).